First ancient mitochondrial human genome from a prepastoralist Southern African

Abstract

The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-­‐speaking forager peoples of Southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semi-­‐ desert regions of Namibia and Botswana, while archeological, historical and genetic evidence promotes a once broader southerly dispersal of click-­‐speaking peoples including southward migrating pastoralists and indigenous marine-­‐foragers. Today extinct, no genetic data has been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa pre-­‐pastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330 year old male skeleton, confirmed via osteological and archeological analysis as practicing a marine-­‐based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-­‐language based sister-­‐ clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-­‐speakers (specifically Ju). Providing the first genomic evidence that pre-­‐pastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.